I'm learning git, and the test case I'm using it for is keeping a repo of my linux profile settings (.bashrc .profile .tmux.conf etc)

on my main machine, the repo is created at the home folder:
base=/home/bvector/
files=/home/bvector/.profile, etc

but when I go to clone the repo on machine2, it goes to /home/bvector/home (as the repo is called home)
base=/home/bvector/home/
files=/home/bvector/home/.profile, etc

Is there a way to have the cloned repo be based in my home folder with all the files in the correct place by default? Everything I've read says you cant clone a repo to a nonempty directory, which would make it a lot more cumbersome to have the repo on multiple machines and be able to seamlessly commit changes.

The --bare option tells it to basically checkout the contents of a normal .git directory (so it won't check out a working copy), and put into the directory ~/.git. You can use git checkout <file> to get individual files, or git reset --hard to replace all your existing files with their equivalent in your git repository, if they exist.